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- PDB-1thf: CYCLASE SUBUNIT OF IMIDAZOLEGLYCEROLPHOSPHATE SYNTHASE FROM THERM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1thf | ||||||
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Title | CYCLASE SUBUNIT OF IMIDAZOLEGLYCEROLPHOSPHATE SYNTHASE FROM THERMOTOGA MARITIMA | ||||||
![]() | HISF PROTEIN | ||||||
![]() | LYASE / THERMOPHILE / TIM-BARREL / HISTIDINE BIOSYNTHESIS / PHOSPHATE-BINDING SITES | ||||||
Function / homology | ![]() imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / L-histidine biosynthetic process / lyase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lang, D.A. / Wilmanns, M. | ||||||
![]() | ![]() Title: Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. Authors: Lang, D.A. / Obmolova, G. / Thoma, R. / Kirschner, K. / Sterner, R. / Wilmanns, M. #1: ![]() Title: A Histidine Gene Cluster of the Hyperthermophile Thermotoga Maritima: Sequence Analysis and Evolutionary Significance Authors: Thoma, R. / Schwander, M. / Liebl, W. / Kirschner, K. / Sterner, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.6 KB | Display | ![]() |
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PDB format | ![]() | 49.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375.9 KB | Display | ![]() |
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Full document | ![]() | 379.3 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 27739.846 Da / Num. of mol.: 1 / Fragment: CYCLASE SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41 % Description: THREE WAVELENGTHS SELENO-METHIONYL MAD EXPERIMENT |
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Crystal grow | pH: 4.8 / Details: pH 4.80 |
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions |
Components of the solutions | *PLUS Conc.: 24.6 mg/ml / Common name: protein |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1997 / Details: MIRROR | ||||||||||||
Radiation | Monochromator: GRAPHITE(002) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.4→38 Å / Num. obs: 38416 / % possible obs: 97.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.1 Å2 / Rsym value: 0.074 / Net I/σ(I): 20.6 | ||||||||||||
Reflection shell | Resolution: 1.4→1.44 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 7.3 / Rsym value: 0.113 / % possible all: 94.6 | ||||||||||||
Reflection | *PLUS Highest resolution: 1.42 Å / Num. obs: 37314 / % possible obs: 95.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.056 | ||||||||||||
Reflection shell | *PLUS Highest resolution: 1.42 Å / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 10.3 |
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Processing
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Refinement | Method to determine structure: ![]() Details: NO ELECTRON DENSITY WAS VISIBLE FOR THE RESIDUES 54-58, THEREFORE THE RESIDUES WERE BUILT STEREOCHEMICALLY, BUT THEIR OCCUPANCIES WERE SET TO ZERO. LOCALISATION OF TWO HETEROCOMPOUNDS ...Details: NO ELECTRON DENSITY WAS VISIBLE FOR THE RESIDUES 54-58, THEREFORE THE RESIDUES WERE BUILT STEREOCHEMICALLY, BUT THEIR OCCUPANCIES WERE SET TO ZERO. LOCALISATION OF TWO HETEROCOMPOUNDS (PHOSPHATES) INTO THE ELECTRON DENSITY. DOUBLE CONFORMATIONS COULD BE OBSERVED FOR THE FOLLOWING RESIDUE ATOMS: OG SER90, NZ LYS99, OG SER122, AND FOR THE ATOMS NE, CZ, NH1, NH2 OF ARG175. VAL79 SHOWS A TRIPLE CONFORMATION FOR ITS CG1 AND CG2 ATOMS.
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Displacement parameters | Biso mean: 16.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
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Refine LS restraints |
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